trees and matrices

Trees and Matrices/gi_choPhyla.tre

@@ -0,0 +1,11 @@
+#NEXUS 
+
+Begin trees;  [Treefile saved Wed May 19 16:04:54 2021]
+[!>Neighbor-joining search settings:
+>  Ties (if encountered) will be broken systematically
+>  Distance measure = mean character difference
+>  All characters have equal weight
+>  (Tree is unrooted)
+]
+tree nj = [&U] ((((((((((((((((((((Arctocephalus_australis:0.01645480,Arctocephalus_tropicalis:0.01744350):0.02409397,((((((Lanius_cristatus:0,Crocidura_hirta:0):0,Phoenicopteridae:0):0.00818086,Grus_japonensis:0.00876830):0.01198776,Melopsittacus_undulatus:0.05580885):0.00724788,Pavo_cristatus:0.02665043):0.00418115,((Mandrillus_leucophaeus:0.03382391,Panthera_leo:0.01702355):0.00327382,Anser_albifrons:0.01367533):0.00641207):0.00662637):0.01036782,(((((Anas_superciliosa:0,Taphozous_perforatus:0):0.01706289,Myotis_ricketti:0.01683541):0.00322300,Rousettus_egyptiacus:0.01372615):0.01053111,(Hipposideros_larvatus:0.01323176,Rhinolophus_affinis:0.00371740):0.01912991):0.01638417,Rattus_exulans:0.03658193):0.01134828):0.00340151,(((Papio_hamadryas:0.02532535,Macaca_sylvanus:0.02552211):0.00917854,((Gorilla_gorilla:0.04857071,Pan_troglodytes:0.07007336):0.02593220,Pan_paniscus:0.04186441):0.02471977):0.01154193,Mandrillus_sphinx:0.03506824):0.01821528):0.00677019,(Carollia_perspicillata:0.02948005,Cavia_porcellus:0.02136741):0.02174875):0.00747643,((((((Mastomys_natalensis:0.01744019,Pipistrellus_pipistrellus:0.01645811):0.00359140,Rhinolophus_ferrumequinum:0.01335775):0.00992584,(Nyctalus_noctula:0.01567315,Eptesicus_serotinus:0.01822515):0.03244704):0.00538899,Alces_alces:0.03698390):0.01802347,Microtus_arvalis:0.03282398):0.00413156,(Red_deer:0.05651278,((((Pongo_abelii:0.01492614,Vulpes_lagopus:0.01897216):0.00359244,(Anser_cygnoides:0.02334843,(Pongo_pygmaeus:0.03529554,Myodes_glareolus:0.03250107):0.01054988):0.00911943):0.01080538,Procyon_lotor:0.00826241):0.00583883,(Apodemus_agrarius:0.01376854,Apodemus_flavicollis:0.02012977):0.02170354):0.01128383):0.00414439):0.00595337):0.00114070,(Lama_glama:0.04311942,Meles_meles:0.02467719):0.02360958):0.00905691,(((Microtus_agrestis:0.03363347,Partridge:0.01721398):0.01285170,((Anguilla_marmorata:0.01784970,Sorex_araneus:0.01604860):0.00354157,(Gorilla_beringei:0.04605500,Canis_latrans:0.00479246):0.01340758):0.01257203):0.00446047,((((Canis_lupus:0.02972633,Lepus_europaeus:0.00417198):0.01020439,Phasianus_colchicus:0.02369391):0.00329330,Struthio_camelus:0.02213043):0.00766408,Tursiops_truncatus:0.02623422):0.00507342):0.01122538):0.00648241,(((Cervus_nippon:0.01893499,Elephas_maximus:0.06581078):0.01855307,(((Zebra:0.00791421,Equus_africanus_asinus:0.04293325):0.00615152,Bison_bison:0.06164509):0.00879198,Macaca_fuscata:0.04205548):0.00687066):0.00963605,((((Sika_deer:0.00674675,Kangaroo:0.01020240):0.02310546,Wombat:0.01079285):0.00377017,Cervus_elaphus:0.04707729):0.01045190,Lemur_catta:0.04039556):0.01790632):0.00261493):0.00386758,Rhinopithecus_bieti:0.03491509):0.00246850,Eulemur_fulvus:0.03142153):0.00405320,(((Marmot:0.01551948,Ferret:0.03532798):0.00914623,(Chinchilla:0.02418633,Phascolarctos_cinereus:0.00971197):0.02475208):0.03163747,(Perca_fluviatilis:0.06029637,(Anser_indicus:0.03380890,(Miniopterus_fuliginosus:0.03058824,Suncus_murinus:0.03720837):0.01703856):0.00750024):0.00332016):0.00452275):0.00746290,(((Sloth_bear:0.01642619,Oreochromis_niloticus:0.03442126):0.00316646,((Tammar_wallaby:0.03233487,Kareius_bicoloratus:0.00156344):0.01026037,(Cyprinus_carpio:0.03684895,Takifugu_obscurus:0.03094766):0.00668878):0.00530812):0.00296772,((((Saimiri_sciureus:0.01178768,Black_Bear:0.02211063):0.01009615,Leopard:0.00685301):0.01500298,Budorcas_taxicolor:0.01889533):0.00639004,Bos_frontalis:0.01055911):0.01398143):0.00531966):0.00689731,(((((((((((((Gallus_gallus:0.10140322,Canis_familiaris:0.10198661):0.01210962,((((Felis_catus:0.07958990,Anas_platyrhynchos:0.05600332):0.00994711,(Macaca_mulatta:0.06896552,Homo_sapiens:0.06662770):0.01547662):0.01001402,Mus_musculus:0.08744360):0.01093344,Sus_scrofa:0.11618520):0.01013614):0.01806963,Rattus_norvegicus:0.05979054):0.01837075,(Anser_anser:0.05148916,Columba_livia:0.06715491):0.01579239):0.00803034,(Corvus:0.04861916,Artibeus_hirsutus:0.01917745):0.01395059):0.00754824,(Eidolon_helvum:0.03879982,Neovison_vison:0.06289509):0.01522718):0.01321998,((Macaca_fascicularis:0.06722430,Rattus_tanezumi:0.01752147):0.00520614,(Rattus_rattus:0.05295339,(Vulpes_vulpes:0.03135635,Meleagris_gallopavo:0.05338941):0.01484322):0.01174301):0.00550851):0.01190363,((Buffalo:0.06452406,Bubalus_bubalis:0.07106916):0.01517180,((((Bos_taurus:0.08509887,Ovis_aries:0.08439266):0.01301026,Equus_caballus:0.10563380):0.02414242,(Camelus_dromedarius:0.00826271,Capra_aegagrus_hircus:0.09343220):0.01823046):0.01956659,Yak:0.07365375):0.03249769):0.01971672):0.01821086,((Giant_panda:0.00614399,Oryctolagus_cuniculus:0.06165262):0.01209425,Marmota_himalayana:0.02180405):0.00870151):0.00716187,Callipepla:0.03371720):0.00789933,Vicugna_pacos:0.04152053):0.01321796,Pheasant:0.00646019):0.01039040,(((Manatee:0,Macropus_eugenii:0):0.01570892,(((Micropterus_salmoides:0.01695743,Rutilus_rutilus:0.01694088):8.4052652e-06,Seriola_dumerili:0.01694075):2.8836525e-05,Siganus_fuscescens:0.01691751):0.00122441):0.00140594,Taeniopygia_guttata:0.01479907):0.00205154):0.00246829):0.00211417,(((Grass_Carp:0.01897244,Danio_rerio:0.01492586):0.00731419,(Salmo:0.06485608,(Bos_indicus:0.06267415,(Oncorhynchus_mykiss:0.07759133,Anguilla_japonica:0.04105274):0.02207161):0.00294053):0.03505869):0.00455198,Tor_tambroides:0.02934632):0.00457188):0.00439925,((((Paralichthys_adspersus:0,Pufferfish:0):0,Tibetan_antelope:0):0,Aplodactylus_punctatus:0):0,Squalius_cephalus:0):0.00517293):0.00330165,(Pseudosciaena_crocea:0.03326737,Chilomycterus_schoepfi:0.01758009):0.01333792):0.00572988,(Hypophthalmichthys_molitrix:0.00532992,(Tilapia:0.02489871,Hamster:0.00899959):0.01161923):0.00682094):0.02284007,Neophocaena_phocaenoides_asiaeorientalis:0.02725540):0.00405412,Octopus_mimus:0.03648709);
+end;

Trees and Matrices/gi_choTangle.tre

@@ -0,0 +1,11 @@
+#NEXUS 
+
+Begin trees;  [Treefile saved Wed May 19 15:19:44 2021]
+[!>Neighbor-joining search settings:
+>  Ties (if encountered) will be broken systematically
+>  Distance measure = mean character difference
+>  All characters have equal weight
+>  (Tree is unrooted)
+]
+tree nj = [&U] (((((((((Gallus_gallus:0.10084503,Mus_musculus:0.14405293):0.01026885,Homo_sapiens:0.13258829):0.02134819,(((Buffalo:0.09093637,Bubalus_bubalis:0.07232893):0.00745376,(((Equus_caballus:0.10938776,Bos_taurus:0.09469388):0.01573129,Ovis_aries:0.12712585):0.02725564,Capra_aegagrus_hircus:0.10539742):0.02826052):0.04087113,(Sus_scrofa:0.11800064,Rattus_norvegicus:0.06567283):0.01014927):0.01277171):0.00946917,(Felis_catus:0.10315689,Canis_familiaris:0.10092474):0.02257803):0.00380909,(Macaca_mulatta:0.08769133,(Anas_platyrhynchos:0.03475765,Pan_troglodytes:0.10809949):0.01434949):0.01978785):0.03075425,Columba_livia:0.08712930):0.01299825,((((((Mastomys_natalensis:0.02825746,Rhinolophus_ferrumequinum:0.01255887):0.03790087,(Rousettus_egyptiacus:0.04081633,Rattus_exulans:0.06122449):0.00291545):0.00892857,(Carollia_perspicillata:0.04702751,Cavia_porcellus:0.01419698):0.02168367):0.02770692,Gorilla_beringei:0.08964002):0.02765731,Eidolon_helvum:0.05142432):0.01840905,Rattus_rattus:0.06194810):0.00436464):0.01285475,Vulpes_vulpes:0.03999636):0.00620445,Meleagris_gallopavo:0.05584001);
+end;

Trees and Matrices/oral_choPhyla.nex

@@ -0,0 +1,58 @@
+#NEXUS
+begin data;
+dimensions ntax=51 nchar=25;
+charlabels Synergistetes Negarnaviricota Basidiomycota Tenericutes Fusobacteria Nematoda Cyanobacteria Proteobacteria Chlamydiae Bacteroidetes Actinobacteria Duplornaviricota Peploviricota Artverviricota Cossaviricota Firmicutes Preplasmiviricota Ascomycota Kitrinoviricota Apicomplexa Parabasalia Pisuviricota Spirochaetes Cressdnaviricota Anelloviridae;
+matrix
+Sus_scrofa 0 1 0 0 1 0 0 1 0 1 1 0 0 0 1 1 0 0 1 0 0 1 0 1 0
+Gorilla_beringei 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0
+Cavia_porcellus 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0
+Rattus_rattus 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
+Rhinolophus_ferrumequinum 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0
+Anas_platyrhynchos 0 1 1 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
+Sapajus_nigritus 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1
+Scotophilus_kuhlii 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
+Vulpes_vulpes 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
+Rousettus_egyptiacus 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
+Wallaby 0 0 0 0 1 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+Sabethes_Gymnothorax 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
+Columba_livia 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+Rattus_exulans 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
+Bos_taurus 0 1 0 1 0 0 0 1 0 0 1 1 0 0 1 1 0 0 1 1 0 1 0 0 0
+Delphinus 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0
+Rattus_norvegicus 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 1 1
+Canis_familiaris 1 1 0 1 1 0 0 1 0 1 1 0 0 0 1 1 0 0 0 0 0 0 1 0 0
+Gallus_gallus 0 1 0 0 0 0 0 1 1 1 1 0 1 0 0 0 1 0 0 0 0 1 0 0 0
+Carollia_perspicillata 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0
+Equus_caballus 0 1 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 1 0 1 0 0
+Carollia_sowelli 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
+Pteropus_giganteus 0 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 1 0 0 0 0 1 0 0 0
+Cynopterus_brachyotis 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
+Papio_anubis 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0
+Felis_catus 0 0 0 0 0 0 0 1 0 1 1 0 0 1 1 1 0 0 0 0 1 0 0 0 0
+Homo_sapiens 1 1 0 0 1 0 0 1 0 1 1 0 0 0 1 1 0 1 0 0 0 1 0 0 0
+Python 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
+Caretta_caretta 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
+Zalophus_californianus 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
+Eidolon_helvum 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1 0 0 0 0 0 0 0 0
+Bothrops_insularis 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0
+Myotis_horsfieldii 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
+Bubalus_bubalis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0
+Mirounga_angustirostris 0 0 0 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+Mus_musculus 0 0 0 0 0 0 0 1 0 1 1 0 0 1 0 1 1 0 0 0 0 1 0 0 0
+Capra_aegagrus_hircus 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 1 0 1 0 0 0
+Meleagris_gallopavo 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+Calidris_fuscicollis 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
+Triaenops_persicus 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0
+Pteropus_lylei 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
+Canis_mesomelas 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
+Macaca_mulatta 0 0 0 0 0 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0 0 0 0
+Mastomys_natalensis 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
+Hipposideros_gigas 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
+Dama_dama 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
+Ovis_aries 0 1 0 1 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
+Buffalo 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
+Pan_troglodytes 0 0 0 0 0 0 1 1 0 1 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0
+Tyto_alba 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
+Pteropus_alecto 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
+;
+end;

Trees and Matrices/oral_choPhyla.tre

@@ -0,0 +1,11 @@
+#NEXUS 
+
+Begin trees;  [Treefile saved Wed May 19 15:20:04 2021]
+[!>Neighbor-joining search settings:
+>  Ties (if encountered) will be broken systematically
+>  Distance measure = mean character difference
+>  All characters have equal weight
+>  (Tree is unrooted)
+]
+tree nj = [&U] (((((((((((((Sus_scrofa:0.09000000,(Canis_familiaris:0.09714286,Homo_sapiens:0.06285714):0.03000000):0.04130435,Bos_taurus:0.13869565):0.06109756,((Felis_catus:0.07404255,Pan_troglodytes:0.04595745):0.03988889,Mus_musculus:0.08011111):0.04390244):0.01315789,Rattus_norvegicus:0.10934211):0.02996228,((Equus_caballus:0.11909722,Ovis_aries:0.04090278):0.02604167,Capra_aegagrus_hircus:0.05395833):0.00128772):0.03354280,(Python:0,Buffalo:0):0.02833220):0.00590255,(((((Gorilla_beringei:0.03524219,(Pteropus_giganteus:0.03931250,Eidolon_helvum:0.08068750):0.04475781):0.00855354,Canis_mesomelas:0.03144646):0.02148397,((((Rattus_rattus:0.06815365,((Anas_platyrhynchos:0.07090909,Columba_livia:0.00909091):0.04363281,Gallus_gallus:0.15636719):0.03184635):0.00723354,Carollia_perspicillata:0.01276646):0.02038989,(((Rhinolophus_ferrumequinum:0,Papio_anubis:0):0.03916667,(Vulpes_vulpes:0.04051136,Bubalus_bubalis:0.03948864):0.00083333):0.03668945,(Scotophilus_kuhlii:0,((Rattus_exulans:0,Carollia_sowelli:0):0,((Cynopterus_brachyotis:0,Myotis_horsfieldii:0):0,(((Calidris_fuscicollis:0,Pteropus_alecto:0):0,Hipposideros_gigas:0):0,Mastomys_natalensis:0):0):0):0):0.00331055):0.01196167):0.00442700,((Rousettus_egyptiacus:0,Pteropus_lylei:0):0.03020996,Triaenops_persicus:0.00979004):0.02134655):0.00505482):0.00637736,Sabethes_Gymnothorax:0.04949369):0.01613131,Meleagris_gallopavo:0.03014106):0.00755425):0.01433183,Sapajus_nigritus:0.08597005):0.01027995,(((Wallaby:0.03964286,Mirounga_angustirostris:0.04035714):0.02273214,Zalophus_californianus:0.05726786):0.01589718,Tyto_alba:0.06410282):0.01646875):0.00603125,Dama_dama:0.05517428):0.00982572,((Cavia_porcellus:0.05500000,Macaca_mulatta:0.06500000):0.01900735,Caretta_caretta:0.02099265):0.01811384):0.05188616,Delphinus:0.01581395):0.00641860,Bothrops_insularis:0.05776744);
+end;

Trees and Matrices/oral_choTangle.tre

@@ -0,0 +1,11 @@
+#NEXUS 
+
+Begin trees;  [Treefile saved Wed May 19 15:20:35 2021]
+[!>Neighbor-joining search settings:
+>  Ties (if encountered) will be broken systematically
+>  Distance measure = mean character difference
+>  All characters have equal weight
+>  (Tree is unrooted)
+]
+tree nj = [&U] ((((((((Sus_scrofa:0.13451087,(Canis_familiaris:0.14583333,Homo_sapiens:0.10416667):0.03215580):0.01728220,Bos_taurus:0.17021780):0.04832176,Rattus_norvegicus:0.11834491):0.00842525,((Felis_catus:0.07333333,Pan_troglodytes:0.05166667):0.04761905,Mus_musculus:0.07738095):0.05407475):0.01809896,(Equus_caballus:0.11869518,Ovis_aries:0.04797149):0.02486979):0.00725446,Capra_aegagrus_hircus:0.06110491):0.02419253,((((((Gorilla_beringei:0.04138692,Vulpes_vulpes:0.04194641):0.00037130,Rhinolophus_ferrumequinum:0.04129537):0.00045268,Bubalus_bubalis:0.04109022):0.01017931,Buffalo:0.03119914):0.02023315,(Rattus_exulans:0,Mastomys_natalensis:0):0.01515299):0.02058309,((((Cavia_porcellus:0.06145833,Macaca_mulatta:0.06354167):0.01944987,Eidolon_helvum:0.10555013):0.02928331,Rousettus_egyptiacus:0.03321669):0.02296193,((Rattus_rattus:0.07253196,Carollia_perspicillata:0.01080137):0.00965983,((Anas_platyrhynchos:0.06336806,Columba_livia:0.01996528):0.05051833,Gallus_gallus:0.15781500):0.03200684):0.01610057):0.00804647):0.01846313):0.00350523,Meleagris_gallopavo:0.03154704);
+end;